ct9b01195_si_001.pdf (902 kB)
A New Lipid Force Field (FUJI)
journal contribution
posted on 2020-05-21, 19:04 authored by Nozomu Kamiya, Megumi Kayanuma, Hideaki Fujitani, Keiko ShinodaTo explore inhomogeneous and anisotropic
systems such as lipid
bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method has
been applied without a conventional isotropic dispersion correction.
As the popular AMBER and CHARMM lipid force fields were developed
using a cutoff scheme, their lipid bilayers unacceptably shrink when
using the LJ-PME method. In this study, a new all-atom lipid force
field (FUJI) was developed on the basis of the AMBER force-field scheme
including the Lipid14 van der Waals parameters. Point charges were
calculated using the restrained electrostatic potentials of many lipid
conformers. Further, torsion energy profiles were calculated using
high-level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ),
following which the molecular mechanical dihedral parameters were
derived through a fast Fourier transform. By incorporation of these
parameters into a new lipid force field without fitting experimental
data, the desired lipid characteristics such as the area per lipid
and lateral diffusion coefficients were obtained through GROMACS molecular
dynamics simulations using the LJ-PME method and virtual hydrogen
sites. The calculated area per lipid and lateral diffusion coefficients
showed satisfactory agreement with experimental data. Furthermore,
the electron-density profiles along the membrane normal were calculated
for pure lipid bilayers, and the resulting membrane thicknesses agreed
well with the experimental values. As the new lipid force field is
compatible with FUJI for protein and small molecules, the new FUJI
force field will offer accurate modeling for complex systems consisting
of various membrane proteins and lipids.